[BiO BB] blast graphical result & gapped alignment

Mike Marchywka marchywka at hotmail.com
Fri Dec 7 10:30:04 EST 2007

>>> The coarse graphics I've encountered for viewing sequences look like it
>> is all generated
>>> html rather than drawn images.

Certainly flybase is using generated html for the coarse stuff,

( I took out "<" and ">" since some program try to execute code excerpts...)

area shape="rect" coords="25,0,65,20" href="?ref=2R;start=9318082;stop=9333256;nav4=1;plugin=" title="recenter" alt="recenter"
area shape="rect" coords="65,0,105,20" href="?ref=2R;start=9318840;stop=9334014;nav4=1;plugin=" title="recenter" alt="recenter"

Looks like hapmap is taking a similar approach but it isn't clear how it is generated.

I've got a fully text output that I'm considering augmenting to generated html for annotation
but I'm trying to concentrate on the automated analysis part rather than interactive

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> Date: Thu, 6 Dec 2007 07:51:42 -0400
> From: carlosjmviana at gmail.com
> To: sowmiya_raj at rediffmail.com
> CC: bbb at bioinformatics.org
> Subject: Re: [BiO BB] blast graphical result & gapped alignment
> You could use GBrowse for display your results. You may include graphical
> results using tracks for each type of results: gapped and ungapped. For
> details and examples:
> * Details
> http://www.gmod.org/wiki/index.php/Gbrowse#Documentation
> http://www.bioperl.org/wiki/Gbrowse
> * Examples
> http://www.hapmap.org/cgi-perl/gbrowse/hapmap_B35/?name=Chr20
> http://flybase.net/cgi-bin/gbrowse/dmel/
> Carlos Juliano.

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